Posted on 11/22/2002 9:09:10 PM PST by forsnax5
NSF awards grants to discover the relationships of 1.75 million species
One of the most profound ideas to emerge in modern science is Charles Darwin's concept that all of life, from the smallest microorganism to the largest vertebrate, is connected through genetic relatedness in a vast genealogy. This "Tree of Life" summarizes all we know about biological diversity and underpins much of modern biology, yet many of its branches remain poorly known and unresolved.
To help scientists discover what Darwin described as the tree's "everbranching and beautiful ramifications," the National Science Foundation (NSF) has awarded $17 million in "Assembling the Tree of Life" grants to researchers at more than 25 institutions. Their studies range from investigations of entire pieces of DNA to assemble the bacterial branches; to the study of the origins of land plants from algae; to understanding the most diverse group of terrestrial predators, the spiders; to the diversity of fungi and parasitic roundworms; to the relationships of birds and dinosaurs.
"Despite the enormity of the task," said Quentin Wheeler, director of NSF's division of environmental biology, which funded the awards, "now is the time to reconstruct the tree of life. The conceptual, computational and technological tools are available to rapidly resolve most, if not all, major branches of the tree of life. At the same time, progress in many research areas from genomics to evolution and development is currently encumbered by the lack of a rigorous historical framework to guide research."
Scientists estimate that the 1.75 million known species are only 10 percent of the total species on earth, and that many of those species will disappear in the decades ahead. Learning about these species and their evolutionary history is epic in its scope, spanning all the life forms of an entire planet over its several billion year history, said Wheeler.
Why is assembling the tree of life so important? The tree is a picture of historical relationships that explains all similarities and differences among plants, animals and microorganisms. Because it explains biological diversity, the Tree of Life has proven useful in many fields, such as choosing experimental systems for biological research, determining which genes are common to many kinds of organisms and which are unique, tracking the origin and spread of emerging diseases and their vectors, bio-prospecting for pharmaceutical and agrochemical products, developing data bases for genetic information, and evaluating risk factors for species conservation and ecosystem restoration.
The Assembling the Tree of Life grants provide support for large multi-investigator, multi-institutional, international teams of scientists who can combine expertise and data sources, from paleontology to morphology, developmental biology, and molecular biology, says Wheeler. The awards will also involve developing software for improved visualization and analysis of extremely large data sets, and outreach and education programs in comparative phylogenetic biology and paleontology, emphasizing new training activities, informal science education, and Internet resources and dissemination.
-NSF-
For a list of the Assembling the Tree of Life grants, see: http://www.nsf.gov/bio/pubs/awards/atol_02.htm
Here are some links and excerpts for lurkers who may be interested in the subject:
Irreducible Contradiction - Mark Perakh. This article is a rebuttal of intelligent design, it alleges that irreducible complexity is but a synonym for randomness. Personally I feel this is sophistry – a misapplication of algorithmic information theory jargon - but lurkers may disagree:
Note, that the definition of complexity in ATP is very different from the definition given by Dembski. The latter defined complexity in terms of the difficulty in solving a problem and identifies complexity as low probability. Dembski's definition provides no clue as to what can make complexity irreducible…
The basic definition relevant to our situation is then as follows: a system is irreducibly complex if the minimum size of a program that is capable of encoding the system approximately equals the size of the system itself. On the other hand, if a system is not random, there exists (at least in principle) a rule prescribing the structure of that system…
Hence, a very important consequence of the basic theorems of ATP is as follows: if a system is indeed irreducibly complex, it is necessarily random. (The proper term is quasi-random, because, strictly speaking, only infinitely large system can be unequivocally determined as random, but this subtle point is not crucial for this discussion.)
In other words, ATP has established that irreducible complexity is just a synonym for (quasi) randomness.
Information, Randomness and Incompleteness
Although Omega is completely random (or infinitely complex) and cannot ever be computed exactly, it can be approximated with arbitrary precision given an infinite amount of time. The complexity of living organisms, it seems to me, could be approximated in a similar way. A sequence of Omega's, which approach Omega , can be regarded as a metaphor for evolution and perhaps could contain the germ of a mathematical model for the evolution of biological complexity.
The Problem "Life" and its "evolution" from the lifeless are fundamental concepts of science. According to Darwin and his followers, we can expect living organisms to evolve under very general conditions. Yet this theory has never been formulated in precise mathematical terms. Supposing Darwin is right, it should be possible to formulate a general definition of "life" and to prove that under certain conditions we can expect it to "evolve." If mathematics can be made out of Darwin, then we will have added something basic to mathematics; while if it cannot, then Darwin must be wrong, and life remains a miracle which has not been explained by science.
The point is that the view that life has spontaneously evolved, and the very concept of life itself, are very general concepts, which it should be possible to study without getting involved in, for example, the details of quantum chemistry. We can idealize the laws of physics and simplify them and make them complete, and then study the resulting universe...
We now turn to Kolmogorov's and Chaitin's proposed definition of randomness or patternlessness. Let us consider once more the scientist confronted by experimental data, a long binary sequence. This time he in not interested in predicting future observations, but only in determining if there is a pattern in his observations, if there is a simple theory that explains them. If he found a way of compressing his observations into a short computer program which makes the computer calculate them, he would say that the sequence follows a law, that it has pattern. But if there is no short program, then the sequence has no pattern--it is random. That is to say, the complexity C(S) of a finite binary sequence S is the size of the smallest program which makes the computer calculate it. Those binary sequences S of a given length n for which C(S) is greatest are the most complex binary sequences of length n, the random or patternless ones. This is a general formulation of the definition…
The main concept of algorithmic information theory is that of the program-size complexity or algorithmic information content of an object (usually just called its "complexity")…
2. Evolution … The ultimate goal, in fact, would be to set up a toy world, to define mathematically what is an organism and how to measure its complexity, and to prove that life will spontaneously arise and increase in complexity with time.
3. Does algorithmic information theory apply to biology? ...One possibility is to ask what is the algorithmic information content of the sequence of bases in a particular strand of DNA. Another possibility is to ask what is the algorithmic information content of the organism as a whole (it must be in discrete symbolic form, e.g., imbedded in a cellular automata model)…
4. Previous work ...In spite of the fact that a satisfactory definition of randomness or lack of structure has been achieved in algorithmic information theory, the first thing that one notices is that it is not ipso facto useful in biology. For applying this notion to physical structures, one sees that a gas is the most random, and a crystal the least random, but neither has any significant biological organization….
5. The halting probability Omega as a model of evolution What is this natural and previously unappreciated example of the evolution of complexity in algorithmic information theory?…
Indeed, to Turing's fundamental theorem in computability theory that the halting problem is unsolvable, there corresponds in algorithmic information theory my theorem … that the halting probability Omega is a random real number. In other words, any program that calculates N bits of the binary expansion of Omega is no better than a table look-up, because it must itself be at least N bits long. I.e., Omega is incompressible, irreducible information.
And it is Omega itself that is our abstract example of evolution! For even though Omega is of infinite complexity, it is the limit of a computable sequence of rational numbers, each of which is of finite but eventually increasing complexity. Here of course I am using the word "complexity" in the technical sense of algorithmic information theory, in which the complexity of something is measured by the size in bits of the smallest program for calculating it…
If you believe evolution is such a process, you do not diminish the role of the creator, but you do not require continuous action by a creator to bring about increasing complexity.
"They're like Napoleon's army in Moscow. They have occupied a lot of territory, and they think they've won the war. And yet they are very exposed in a hostile climate with a population that's very much unfriendly."
"That's the case with the Darwinists in the United States. The majority of the people are skeptical of the theory. And if the theory starts to waver a bit, it could all collapse, as Napoleon's army did in a rout."
One problem with Dembski's writings is that he sometimes uses this definition of complexity and sometimes uses the opposite. Dembski's continual switching of meanings makes his writings useless.
my assertion -- that there exist streams of data which cannot be determined to be the result of a simple algorithm, but which are.
Actually, the Chaitin material indicates that Omega is true randomness and cannot be the result of a simple algorithm. He likens Omega to the diversity of biological life. It appears this is the basis for Perakh's dismissal of "irreducible complexity."
To the contrary notwithstanding, the algorithmic information theorists continue to look for the underlying algorithms and indicate it should be there in support of Darwin's theory. I find the apparent contradiction strangely interesting.
If you believe evolution is such a process, you do not diminish the role of the creator, but you do not require continuous action by a creator to bring about increasing complexity.
I am actually on the extreme of this debate. I fully expect a primordial algorithm (a mathematical theory of everything) to be found. I expect it to be rooted in the inception of the universe, the Big Bang - and to be so algorithmically complex (step by step instruction) that it will defy a naturalist explanation.
Even further, I expect that algorithm to manifest the fields in some form of harmonics. People who are inclined to randomness in biological evolution would be extremely disappointed, but I believe finding such an algorithm will be helpful across the board - natural history, astro-physics, astrobiology, medicine, chemistry, physics, etc. And of course, teleology would breathe a sigh of relief!
You see they hide behind the fact it is not possible to obtain a proof of the relationship between "bones" separated by millions of years. However, that does not stop them from expecting proof from others.
That is the problem, isn't it? Both sides reach a point of faith - one in a hypothesis and the other in theology.
One problem with Dembski's writings is that he sometimes uses this definition of complexity and sometimes uses the opposite.
I agree that it would certainly benefit his work to define the terms as he uses them (as Chaitin does.) Leaving it open to the reader can create a lot of misunderstanding.
One of the stronger viewpoints that Shapiro has is his apparent utter rejection of the gradualist, stochastic evolution of organisms. From that premise it is difficult to understand how a computing machine could come into being using a gradualist, stochastic mechanism.
That's nothing more than a rehash of the argument that it's difficult to see how an eye evolved, or a flagella, or any other thing that's been thought to present difficulty to evolutionary theory. The fact that satisfactory explanations have been consistently found in other cases suggests that a satisfactory explanation exists here also.
In any case, saying that "gradual, stochastic processes" can't account for the evolution of organisms doesn't mean a non-material agent is suddenly required. My mail isn't delivered by gradual, stochastic processes, but does that mean it has a non-material cause? Of course not.
It seems to me that the development of such abilities might account very well for such events as the Cambrian explosion - stochastic processes produce simple organisms, which eventually have the ability to self-modify. Since such a trait is obviously adaptive, the pace of evolution jumps far and above what we might expect from simple random mutations, causing rapid developments of diverse organisms. But nowhere in there is a non-material agent required or expected.
Shapiro's speculation is entirely and consistently naturalistic. Internal information-processing and self-modification implicitly denies non-material agency as a cause of change by explaining how organisms change themselves, pulling themselves up by the bootstraps, so to speak. If I can change my own genome in response to changing environments, non-material agents are hardly required to do it for me. And to deny that stochastic processes could produce such a trait is tantamount to denying that stochastic processes can do anything at all - something that I highly doubt Shapiro, or anyone else, is prepared to suggest.
All I need do is post his words.
Localized random mutation, selection operating "one gene at a time" (John Maynard Smith's formulation), and gradual modification of individual functions are unable to provide satisfactory explanations for the molecular data, no matter how much time for change is assumed.
No matter how much time.
Of course, I don't actually know anyone who argues that point mutations and genetic drift are responsible for everything any more. Shapiro has, I am sure, heard of lateral transfers, which are A) relatively well-documented, and; B) don't necessarily operate "one gene at a time", and; C) can account for the rapid introduction of new functions into an organism. So, where exactly is non-material agency required here?
The situations aren't at all epistemologically identical. The hypothesis does, after all, have the feature of being a natural explanation, which can -- at least in principle -- be tested, and perhaps disproved. The theological proposition is in a privileged position of being untestable. I suspect is not appropriate to use the word "faith" for both propositions. (I suppose this sounds like a mere semantic quibble, but I think it's more than that.)
So if evolutionists claim that Christianity and evolution are not irreconcilable then why do they attack Christianity and the Bible whenever they start losing on the scientific side of these threads. There can only be one reason:
I can't recall anyone actually attacking Christianity, but there have certainly been objections to literal interpretations of the Bible. Reading Genesis as an allegory allows God the leeway of creating the world in more than six days. I think you should give Him the benefit of the doubt on that. Unless, of course, you think He couldn't have done it that way.
Why do evolutionists fight so hard against those who deny abiogenesis (that life was not created)? After all they also say that evolution has nothing to do with how life began. There can only be one reason:
Well, there's this thing about beginnings. You want life to be created by existing life, so you're kind of fudging the "first life" thing. Or maybe God is not alive? And the fact that "evolution" doesn't include "abiogenesis" is just simply that evolution describes change, not beginnings.
Why do evolutionists do not give Christians at least one species amongst over ten million to say that it was created as the Bible says? Why so insistent on denying that man may at least be the one unique species which was created? Why not give Christians that much when it should be so little to them - one species in ten million? Only one possible reason:
This is a really odd proposal. I can see you arguing for ALL species being created, or for all "kinds" being created, but what would ONE species do for you? As to the question itself (why not one?), because that would make no sense to either side of the discussion.
Why such insistence that Intelligent Design cannot be true? Why deny the possibility that in one little instance perhaps one little function, in a measley bacteria which no one really cares for anyways could possibly have been intelligently designed? It is such a little thing after all. There can only be one reason:
If an Intelligent Designer designed anything at all, then everything could have been designed. If everything was designed, then nothing is related. If nothing is related, then all of our biological inferences are imaginary. ID simply creates more problems than it solves. Stick with God.
Why indeed must evolutionists deny that anything could have been designed? Why insist that everything is a result of a random materialistic process? Why try to even prevent such an explanation from being intelligently discussed? Why can't they give an inch, a millimiter, or anything at all to those who believe in an Almighty? There can only be one reason:
More of the same rant. Are we not discussing this? And you're certainly not in a position to complain about someone not giving an inch. What's your rationale for being always right?
Just as a disclaimer, I am an agnostic. I don't believe in the God of the Bible, but I am open to the idea that this universe was created by an intelligence. I see no evidence for it, but our viewpoint is limited and our history is short. I am interested in any and all ideas.
And I think, on the whole, that Christianity is a good thing.
This obviously was not the best analogy but I appreciate the fact that you tried to understand it in its context (and did).
The “Design Theory” has been around for a long time (arguably western science was based on it) but the “intelligent design theory” is new. I like the fact that you do not totally reject design altogether (just waiting for better evidence)
First let me say that evolution does not bother me as much as naturalism. I too have Christian friends that believe evolution to be the source of mankind and I don’t question their faith. But the fact is, they must acknowledge design at some point.
Now back to my analogy…
What I find interesting about science as it stands now is that it only allows for natural explanations. Our reality can only be attributed to natural causes… hmmm… and this is based on human thought… But what do we know about our own self-consciousness? Is this physical or non-physical - non-natural?
The major tool used by the scientific community to say that everything is due to natural causes is mankind’s very own consciousness. Yet this same self-consciousness has not been attributed to natural causes. Many say it may never.
So this is the rock (in the analogy) that can cause the educated (as well as the uneducated) to follow a different path. It could logically be self evident to some that natural causes do not explain even the most obvious thing in ones life, i.e. consciousness. (If one is not sure of his own consciousness, what can he be sure of?)
But back to design… as I said, “What are you looking for?”
If you look for only natural causes for everything that is what you will find. But if someone sees design and purpose beyond natural explanations and you chose to dispute what they see – start with your own self-consciousness, then get back to them.
Believe what you want to believe and see what you what to see… I do not want to impose my views on anyone nor do I ‘pretend’ to think I could… Naturalism in the scientific ‘commune’ does this – not me…
Well, then what is all the fuss about. It seems as if he has problems with something that does not exist. If lateral transfer or some such other mechanism that is consistent with Darwinism can explain the formation of the things he says cannot be explained, why the heck is he saying anything? He has a problem. And that problem is with Darwinism. It is plainly evident. The question of the necessity of a non-material agency is not addressed. That question is open to Shapiro as I have pointed out. I doubt that he adheres to the ID perspective, yet it seems to me that he has not ruled it out.
Because he's arguing in favor of his theories of self-modification, as opposed to point mutations and genetic drift being used to account for the entirety of the diversity of life. It seems to me - and I'm sure you'll correct me if I'm wrong - that you are reading him as saying that stochastic processes can't account for anything. But it is clear that he is arguing that stochastic processes can't account for everything, and thus he proposes an alternate mechanism to account for the bulk of the diversity of life. An alternate mechanism which is, it seems clear, entirely naturalistic.
The question of the necessity of a non-material agency is not addressed. That question is open to Shapiro as I have pointed out. I doubt that he adheres to the ID perspective, yet it seems to me that he has not ruled it out.
I don't agree. It seems to me that he has implicitly ruled out external agency in favor of internal information-processing abilities and self-modifications by organisms. If he's right about these internal abilities of organisms, what is there for an external agent to do?
I meant the word faith to mean "something that is believed with strong conviction." That implies "without doubt or question" and thus usually is associated with religious belief. Perhaps it would have suited you better if I had said:
That is the problem, isn't it? Both sides reach a point of strong conviction - one in a hypothesis and the other in theology.
All hypotheses, IMHO, should be subject to testing and especially, to falsification - or else they risk becoming ideology. I would that the criteria for falsification of the theory of biological evolution were specified and published (if they are, I haven't found them thus far.)
Here is an interesting link that discusses Faith and Reason
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